From 062268db3d06c20830aa52510666941c1470f7ae Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 2 Aug 2011 13:21:25 +0200
Subject: [PATCH] Added new member description_ to chain. With get/ set
functions and test.
---
modules/io/src/mol/mmcif_reader.cc | 8 +++++++-
modules/io/src/mol/mmcif_reader.hh | 4 +++-
modules/mol/base/src/chain_base.cc | 4 ++++
modules/mol/base/src/chain_base.hh | 5 +++++
modules/mol/base/src/editor_base.cc | 6 ++++++
modules/mol/base/src/editor_base.hh | 6 ++++++
modules/mol/base/src/impl/chain_impl.cc | 3 ++-
modules/mol/base/src/impl/chain_impl.hh | 17 +++++++++++++++++
modules/mol/base/tests/test_chain.cc | 16 +++++++++++++---
9 files changed, 63 insertions(+), 6 deletions(-)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 3bac82e55..7fba25293 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -154,7 +154,8 @@ bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
// mandatory items
this->TryStoreIdx(E_ID, "id", header);
// optional
- indices_[E_TYPE] = header.GetIndex("type");
+ indices_[E_TYPE] = header.GetIndex("type");
+ indices_[DETAILS] = header.GetIndex("details");
return true;
}
/*else if (header.GetCategory()=="entity_poly") {
@@ -451,6 +452,11 @@ void MMCifParser::ParseEntity(const std::vector<StringRef>& columns)
store = true;
}
+ // description
+ if (indices_[DETAILS] != -1) {
+ desc.details = columns[indices_[E_TYPE]].str();
+ }
+
if (store) {
entity_desc_map_.insert(
MMCifEntityDescMap::value_type(columns[indices_[E_ID]].str(),
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 529702a74..73e378aeb 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -186,7 +186,8 @@ private:
/// \enum items of the entity category
typedef enum {
E_ID, ///< unique identifier
- E_TYPE ///< polymer, non-polymer or water
+ E_TYPE, ///< polymer, non-polymer or water
+ DETAILS ///< special aspects of the entity
} EntityItems;
/// \enum categories of the mmcif format
@@ -199,6 +200,7 @@ private:
/// \struct keeping track of entity information
typedef struct {
ChainType type; ///< characterise entity
+ String details; ///< description of this entity
} MMCifEntityDesc;
typedef std::map<String, MMCifEntityDesc> MMCifEntityDescMap;
diff --git a/modules/mol/base/src/chain_base.cc b/modules/mol/base/src/chain_base.cc
index 4147ed532..1f5b04cd0 100644
--- a/modules/mol/base/src/chain_base.cc
+++ b/modules/mol/base/src/chain_base.cc
@@ -48,6 +48,10 @@ ChainType ChainBase::GetChainType() const {
return impl_->GetChainType();
}
+String ChainBase::GetChainDescription() const {
+ return impl_->GetChainDescription();
+}
+
void ChainBase::CheckValidity() const {
if (!impl_)
throw InvalidHandle();
diff --git a/modules/mol/base/src/chain_base.hh b/modules/mol/base/src/chain_base.hh
index ca9e45724..5410ada9f 100644
--- a/modules/mol/base/src/chain_base.hh
+++ b/modules/mol/base/src/chain_base.hh
@@ -65,6 +65,11 @@ public:
/// \return chain type of ChainType
ChainType GetChainType() const;
+ /// \brief Get information about a chain.
+ ///
+ /// \return description
+ String GetChainDescription() const;
+
const impl::ChainImplPtr& Impl() const {
return impl_;
}
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index b959d23ea..c9fa92bd4 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -88,6 +88,12 @@ void EditorBase::SetChainType(ChainHandle chain, const ChainType type)
chain.Impl()->SetChainType(type);
}
+void EditorBase::SetChainDescription(ChainHandle chain, const String desc)
+{
+ CheckHandleValidity(chain);
+ chain.Impl()->SetChainDescription(desc);
+}
+
AtomHandle EditorBase::InsertAtom(ResidueHandle res, const String& name,
const geom::Vec3& pos, const String& ele,
Real occupancy, Real b_factor,
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index cb009474c..cd8c811ca 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -162,6 +162,12 @@ public:
/// \param type type of the chain
void SetChainType(ChainHandle chain, const ChainType type);
+ /// \brief Assign a description to a chain.
+ ///
+ /// \param chain chain to assign to
+ /// \param desc description
+ void SetChainDescription(ChainHandle chain, const String desc);
+
/// \brief Delete all atoms of residue
///
/// All associated torsions and bonds will also be removed
diff --git a/modules/mol/base/src/impl/chain_impl.cc b/modules/mol/base/src/impl/chain_impl.cc
index 558eb2c52..a96ce571c 100644
--- a/modules/mol/base/src/impl/chain_impl.cc
+++ b/modules/mol/base/src/impl/chain_impl.cc
@@ -37,7 +37,8 @@ ChainImpl::ChainImpl(const EntityImplPtr& e, const String& name):
name_(name),
residue_list_(),
in_sequence_(true),
- chain_type_(CHAINTYPE_UNKNOWN)
+ chain_type_(CHAINTYPE_UNKNOWN),
+ description_()
{}
String ChainImpl::GetName() const
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index 4758297b0..31bd36879 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -64,6 +64,22 @@ public:
return chain_type_;
}
+ /// \brief Assign a description to a chain.
+ ///
+ /// \param desc description
+ void SetChainDescription(const String desc)
+ {
+ description_ = desc;
+ }
+
+ /// \brief Get information about a chain
+ ///
+ /// \return description
+ String GetChainDescription() const
+ {
+ return description_;
+ }
+
/// \brief append new residue with exactly the same parameters as res, but
/// no atoms and bonds
ResidueImplPtr AppendResidue(const ResidueImplPtr& res);
@@ -152,6 +168,7 @@ private:
/// to optimize residue by number lookup.
bool in_sequence_;
ChainType chain_type_;
+ String description_; ///< special aspects of the chain
};
}}} // ns
diff --git a/modules/mol/base/tests/test_chain.cc b/modules/mol/base/tests/test_chain.cc
index 80b729d75..b866ecd00 100644
--- a/modules/mol/base/tests/test_chain.cc
+++ b/modules/mol/base/tests/test_chain.cc
@@ -204,9 +204,9 @@ BOOST_AUTO_TEST_CASE(rename_chain)
BOOST_AUTO_TEST_CASE(chain_type)
{
- EntityHandle eh=CreateEntity();
- XCSEditor e=eh.EditXCS();
- ChainHandle ch1=e.InsertChain("A");
+ EntityHandle eh = CreateEntity();
+ XCSEditor e = eh.EditXCS();
+ ChainHandle ch1 = e.InsertChain("A");
BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_UNKNOWN);
e.SetChainType(ch1, CHAINTYPE_POLY);
@@ -235,4 +235,14 @@ BOOST_AUTO_TEST_CASE(chain_type)
BOOST_CHECK(ch1.GetChainType() == CHAINTYPE_UNKNOWN);
}
+BOOST_AUTO_TEST_CASE(chain_description)
+{
+ EntityHandle eh=CreateEntity();
+ XCSEditor e = eh.EditXCS();
+ ChainHandle ch1 = e.InsertChain("A");
+ String description = "Very important information";
+ e.SetChainDescription(ch1, description);
+ BOOST_CHECK(ch1.GetChainDescription() == description);
+}
+
BOOST_AUTO_TEST_SUITE_END()
--
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